plot_overrep_kmer {qckitfastq} | R Documentation

## Create a box plot of the log2(observed/expected) ratio across the length of the sequence as well as top overrepresented kmers. Only ratios greater than 2 are included in the box plot. Default is 20 bins across the length of the sequence and the top 2 overrepresented kmers, but this can be changed by the user.

### Description

Create a box plot of the log2(observed/expected) ratio across the length of the sequence as well as top overrepresented kmers. Only ratios greater than 2 are included in the box plot. Default is 20 bins across the length of the sequence and the top 2 overrepresented kmers, but this can be changed by the user.

### Usage

    plot_overrep_kmer(overkm, bins = 20, top_num = 2, output_file = NA)

### Arguments

`overkm` | data frame with columns pos, obsexp_ratio, and kmer
`bins` | number of intervals across the length of the sequence
`top_num` | number of most overrepresented kmers to plot
`output_file` | File to write plot to. Will not write to file if NA. Default NA.

### Value

A box plot of the log2(observed/expected ratio) across the length of the sequence

### Examples

    infile <- system.file("extdata", "test.fq.gz",
        package = "qckitfastq")
    over_km <- overrep_kmer(infile,k=4)
    plot_overrep_kmer(over_km)

[Package qckitfastq version 1.6.0 Index]